﻿#region Copyright information
// 
// Copyright © 2012-2013 Yongkee Cho. All rights reserved.
// 
// This code is a part of the SubnetworkToolkit and governed under the terms of the
// GNU Lesser General  Public License (LGPL) version 2.1 which accompanies this distribution.
// For more information on the LGPL, please visit http://bol.codeplex.com/license.
// 
// - Filename: Options.cs
// - Author: Yongkee Cho
// - Email: yongkeecho@outlook.com
// - Date Created: 2013-01-30 2:55 PM
// - Last Modified: 2013-01-30 3:21 PM
// 
#endregion
using System.Text;
using CommandLine;

namespace SubnetworkToolkit.Filter
{
    public class Options
    {
        [Option("g", "gmt file", HelpText = "Specify a gmt file.")]
        public string GmtFile { get; set; }

        [Option("o", "output", HelpText = "Specify an output file.")]
        public string OutputFile { get; set; }

        [OptionList("n", "include", HelpText = "Include only sub-networks that contain genes you specify.")]
        public string[] Include { get; set; }

        [OptionList("x", "exclude", HelpText = "Exclude sub-networks that contain genes you specify.")]
        public string[] Exclude { get; set; }

        [HelpOption(HelpText = "Dispaly this help screen.")]
        public string GetUsage()
        {
            var help = new StringBuilder();
            help.AppendLine("Usage : filter [OPTION]");
            help.AppendLine("Options:");
            help.AppendLine("    -g           gmt file");
            help.AppendLine("    -o           output file");
            help.AppendLine("    -n           include genes");
            help.AppendLine("    -x           exclude genes");
            return help.ToString();
        }
    }
}
